The Welsh side have been stuck in Cape Town since South Africa was added to the UK government’s travel red list.
The Blue and Blacks and Munster had hoped to join Zebre Parma in leaving on Sunday aboard a charter flight but two positive cases stopped that.
Munster will be unable to leave, having reported nine new cases among their players and staff following the latest round of PCR testing.
Cardiff’s players and staff who are negative will return to the UK on a charter plane and quarantine in a government hotel for 10 days.
A statement from the Welsh club read: “Cardiff Rugby plan to depart Cape Town on Thursday morning after the club secured a charter flight and quarantine accommodation in England.
“The Blue and Blacks’ travelling contingent, which includes 15 full Welsh internationals, had been left stranded in the city after South Africa was placed on the UK’s red list and borders were closed to arrivals from six countries on the continent – now 10 in Wales.
“It had been hoped they would be able to depart on a flight with Munster Rugby, Scarlets and Zebre Parma on Sunday, but two positive cases ruled out the departure.
“However, working in collaboration with the United Rugby Championship and the Welsh Rugby Union, a charter flight has been confirmed for Thursday morning. Upon arrival in England, Wales’ capital city club will then begin a 10-day period of isolation in a UK Government Covid-19 hotel.
“Those remaining in South Africa will undertake 10-days quarantine in a South African Covid-19 hotel and will be repatriated to the UK as soon as possible.
“Cardiff Rugby would like to thank the URC, WRU and government agencies in South Africa for their support at this difficult time.”
Munster reported nine positive coronavirus cases among their players and staff.
In a statement posted on the Irish province’s official website, Munster said: “Munster’s latest round of PCR testing has identified nine positive cases.
“The group, including staff and players, will move to the designated quarantine hotel in Cape Town, joining the first player who tested positive on Sunday.
“The remaining party of 38 have all returned negative results and continue to individually isolate in their rooms where they have been based since Sunday night.
“As outlined by the Irish government on Monday, those that have received negative results have clearance to travel from the South African authorities.
“In taking every precaution, the touring party have completed another round of PCR testing this morning, the third in less that 60 hours, and will wait on results ahead of next steps.
“The 10 members of the group who have tested positive will remain in Cape Town until the end of their isolation period. While the individuals were disappointed on receiving the news, they are thankfully well and will continue to be monitored medically at this time.
“We understand this is a challenging situation and would like to thank families, friends, colleagues and our rugby community for the many messages of best wishes.”
Scarlets players and staff are currently isolating at a Belfast hotel, while Parma’s squad are doing likewise in Italy.
The Heineken Champions Cup is due to kick off on 10 December, with Cardiff hosting European champions Toulouse the following day and Munster visiting Wasps 24 hours later.
The Scarlets are scheduled to begin their European campaign against Bristol at Ashton Gate on 11 December, with Munster and Cardiff also facing 10 days of hotel quarantine when they eventually arrive back.
Teams who are unable to fulfil European Cup fixtures face forfeiting the game under strict tournament rules, and it is understood that competition organisers currently have no plans to postpone games.
Such a stance, though, drew criticism last season after a handful of coronavirus-related cancellations saw teams responsible handed 28-0 defeats.